auto_annot_Martin2019_with_Smillie2019_Type

In [1]:
import besca as bc
import pkg_resources
./conda/envs/besca_test/lib/python3.6/site-packages/scanpy/api/__init__.py:6: FutureWarning: 

In a future version of Scanpy, `scanpy.api` will be removed.
Simply use `import scanpy as sc` and `import scanpy.external as sce` instead.

  FutureWarning,

Specify folders where .h5ad files are found and their names.

The datasets that are already annotated and should be used for training. If you only use one dataset please use list of one.

In [2]:
# the path to the datasets
train_dataset_paths = [pkg_resources.resource_filename('besca', 'datasets/data')]
#the names of the h5ad files
train_datasets = ['Smillie2019_processed.h5ad']

The dataset of interest that should be annotated.

In [3]:
test_dataset = 'Martin2019_processed.h5ad'
test_dataset_path =  pkg_resources.resource_filename('besca', 'datasets/data')

Give your analysis a name.

In [4]:
analysis_name = 'auto_annot_Martin2019_with_Smillie2019_Type' 

Now specify parameters

Specify column name of celltype annotation you want to train on.

In [5]:
celltype ='Type' 

Choose a method:

  • linear: Support Vector Machine with Linear Kernel
  • sgd: Support Vector Machine with Linear Kernel using Stochastic Gradient Descent
  • rbf: Support Vector Machine with radial basis function kernel. Very time intensive, use only on small datasets.
  • logistic_regression: Standard logistic classifier iwth multinomial loss.
  • logistic_regression_ovr: Logistic Regression with one versus rest classification.
  • logistic_regression_elastic: Logistic Regression with elastic loss, cross validates among multiple l1 ratios.
In [6]:
method = 'logistic_regression'

Specify merge method if using multiple training datasets. Needs to be either scanorama or naive.

In [7]:
merge = 'scanorama'

Decide if you want to use the raw format or highly variable genes. Raw increases computational time and does not necessarily improve predictions.

In [8]:
use_raw = False

You can choose to only consider a subset of genes from a signature set.

In [9]:
genes_to_use = 'all'

Read in all training and the testing set.

In [10]:
adata_trains, adata_pred, adata_orig = bc.tl.auto_annot.read_data(train_paths = train_dataset_paths,train_datasets= train_datasets, test_path=  test_dataset_path, test_dataset= test_dataset, use_raw = use_raw)
Transforming to str index.
Reading files
Transforming to str index.
In [11]:
adata_trains[0].obs
Out[11]:
CELL Cluster Health Location Subject celltype_highlevel nGene nUMI original_name percent_mito n_counts n_genes batch leiden dblabel celltype cluster_celltype Type
0 N7.EpiA.AAGCAAGAGTCAAC-Epi Cycling TA Non-inflamed Epi N7 Epi 1507 7428 N7.EpiA.AAGCAAGAGTCAAC 0.057351 7428.0 1507 N7 8 proliferating transit amplifying cell epithelial cell 8: epithelial cell Epithelial
1 N7.EpiA.ACGAGGGAGCTGAT-Epi Enterocyte Progenitors Non-inflamed Epi N7 Epi 828 2877 N7.EpiA.ACGAGGGAGCTGAT 0.009037 2877.0 828 N7 0 enterocyte progenitor epithelial cell 0: epithelial cell Epithelial
2 N7.EpiA.ACGTTTACTGGTAC-Epi Immature Enterocytes 2 Non-inflamed Epi N7 Epi 2318 15332 N7.EpiA.ACGTTTACTGGTAC 0.133707 15332.0 2318 N7 7 immature enterocyte enterocyte 7: enterocyte Epithelial
3 N7.EpiA.AGAGAATGGTCATG-Epi Enterocyte Progenitors Non-inflamed Epi N7 Epi 884 3498 N7.EpiA.AGAGAATGGTCATG 0.002001 3498.0 884 N7 7 enterocyte progenitor enterocyte 7: enterocyte Epithelial
4 N7.EpiA.AGAGCGGAGTATGC-Epi TA 1 Non-inflamed Epi N7 Epi 858 3261 N7.EpiA.AGAGCGGAGTATGC 0.003067 3261.0 858 N7 0 transit amplifying cell epithelial cell 0: epithelial cell Epithelial
5 N7.EpiA.AGATTAACGCCATA-Epi Cycling TA Non-inflamed Epi N7 Epi 2743 20160 N7.EpiA.AGATTAACGCCATA 0.097123 20160.0 2743 N7 8 proliferating transit amplifying cell epithelial cell 8: epithelial cell Epithelial
6 N7.EpiA.AGGATGCTTACAGC-Epi TA 2 Non-inflamed Epi N7 Epi 812 2764 N7.EpiA.AGGATGCTTACAGC 0.003618 2764.0 812 N7 0 transit amplifying cell epithelial cell 0: epithelial cell Epithelial
7 N7.EpiA.AGGTACACAGACTC-Epi Cycling TA Non-inflamed Epi N7 Epi 3109 23926 N7.EpiA.AGGTACACAGACTC 0.062192 23926.0 3109 N7 8 proliferating transit amplifying cell epithelial cell 8: epithelial cell Epithelial
8 N7.EpiA.AGTCTACTTCTCTA-Epi TA 2 Non-inflamed Epi N7 Epi 1945 12338 N7.EpiA.AGTCTACTTCTCTA 0.083806 12338.0 1945 N7 0 transit amplifying cell epithelial cell 0: epithelial cell Epithelial
9 N7.EpiA.ATAGTCCTTAACCG-Epi TA 2 Non-inflamed Epi N7 Epi 2172 13869 N7.EpiA.ATAGTCCTTAACCG 0.128055 13869.0 2172 N7 0 transit amplifying cell epithelial cell 0: epithelial cell Epithelial
10 N7.EpiA.ATATACGAAGTACC-Epi TA 2 Non-inflamed Epi N7 Epi 1245 5765 N7.EpiA.ATATACGAAGTACC 0.052559 5765.0 1245 N7 0 transit amplifying cell epithelial cell 0: epithelial cell Epithelial
11 N7.EpiA.ATTCCAACTTTGGG-Epi TA 2 Non-inflamed Epi N7 Epi 1380 7240 N7.EpiA.ATTCCAACTTTGGG 0.072238 7240.0 1380 N7 0 transit amplifying cell epithelial cell 0: epithelial cell Epithelial
12 N7.EpiA.ATTCGACTGCATAC-Epi Cycling TA Non-inflamed Epi N7 Epi 1043 3617 N7.EpiA.ATTCGACTGCATAC 0.004147 3617.0 1043 N7 8 proliferating transit amplifying cell epithelial cell 8: epithelial cell Epithelial
13 N7.EpiA.ATTGAAACCTATGG-Epi TA 1 Non-inflamed Epi N7 Epi 959 4008 N7.EpiA.ATTGAAACCTATGG 0.003743 4008.0 959 N7 0 transit amplifying cell epithelial cell 0: epithelial cell Epithelial
14 N7.EpiA.CAAGCCCTTGACAC-Epi TA 2 Non-inflamed Epi N7 Epi 1082 4640 N7.EpiA.CAAGCCCTTGACAC 0.067672 4640.0 1082 N7 0 transit amplifying cell epithelial cell 0: epithelial cell Epithelial
15 N7.EpiA.CACGATGAGCTAAC-Epi Cycling TA Non-inflamed Epi N7 Epi 1082 3790 N7.EpiA.CACGATGAGCTAAC 0.002111 3790.0 1082 N7 8 proliferating transit amplifying cell epithelial cell 8: epithelial cell Epithelial
16 N7.EpiA.CAGACATGTTTGTC-Epi Cycling TA Non-inflamed Epi N7 Epi 849 2844 N7.EpiA.CAGACATGTTTGTC 0.001055 2844.0 849 N7 0 proliferating transit amplifying cell epithelial cell 0: epithelial cell Epithelial
17 N7.EpiA.CAGGAACTCGTTAG-Epi Secretory TA Non-inflamed Epi N7 Epi 1799 13535 N7.EpiA.CAGGAACTCGTTAG 0.103288 13535.0 1799 N7 6 transit amplifying cell goblet cell 6: goblet cell Epithelial
18 N7.EpiA.CCACGGGAGTTACG-Epi TA 2 Non-inflamed Epi N7 Epi 1097 4700 N7.EpiA.CCACGGGAGTTACG 0.027234 4700.0 1097 N7 0 transit amplifying cell epithelial cell 0: epithelial cell Epithelial
19 N7.EpiA.CGAGGAGACGAGTT-Epi TA 2 Non-inflamed Epi N7 Epi 1007 3832 N7.EpiA.CGAGGAGACGAGTT 0.071764 3832.0 1007 N7 0 transit amplifying cell epithelial cell 0: epithelial cell Epithelial
20 N7.EpiA.CGCTAAGATAGCGT-Epi Immature Goblet Non-inflamed Epi N7 Epi 935 4147 N7.EpiA.CGCTAAGATAGCGT 0.005305 4147.0 935 N7 6 immature goblet cell goblet cell 6: goblet cell Epithelial
21 N7.EpiA.CGGACTCTTGCCTC-Epi TA 2 Non-inflamed Epi N7 Epi 1720 9256 N7.EpiA.CGGACTCTTGCCTC 0.085566 9256.0 1720 N7 0 transit amplifying cell epithelial cell 0: epithelial cell Epithelial
22 N7.EpiA.CGTCCATGGGTTCA-Epi TA 2 Non-inflamed Epi N7 Epi 804 2824 N7.EpiA.CGTCCATGGGTTCA 0.001771 2824.0 804 N7 0 transit amplifying cell epithelial cell 0: epithelial cell Epithelial
23 N7.EpiA.CTGATGGACCCTCA-Epi Secretory TA Non-inflamed Epi N7 Epi 944 5081 N7.EpiA.CTGATGGACCCTCA 0.031096 5081.0 944 N7 6 transit amplifying cell goblet cell 6: goblet cell Epithelial
24 N7.EpiA.CTTAAGCTTACGAC-Epi Cycling TA Non-inflamed Epi N7 Epi 2356 15497 N7.EpiA.CTTAAGCTTACGAC 0.066271 15497.0 2356 N7 8 proliferating transit amplifying cell epithelial cell 8: epithelial cell Epithelial
25 N7.EpiA.GAGCTCCTACCACA-Epi TA 2 Non-inflamed Epi N7 Epi 1240 5349 N7.EpiA.GAGCTCCTACCACA 0.005235 5349.0 1240 N7 0 transit amplifying cell epithelial cell 0: epithelial cell Epithelial
26 N7.EpiA.GAGCTCCTGCCTTC-Epi Cycling TA Non-inflamed Epi N7 Epi 3145 25630 N7.EpiA.GAGCTCCTGCCTTC 0.112563 25630.0 3145 N7 6 proliferating transit amplifying cell goblet cell 6: goblet cell Epithelial
27 N7.EpiA.GATGCAACACGCAT-Epi TA 2 Non-inflamed Epi N7 Epi 981 4075 N7.EpiA.GATGCAACACGCAT 0.006871 4075.0 981 N7 0 transit amplifying cell epithelial cell 0: epithelial cell Epithelial
28 N7.EpiA.GCGAGAGATCGTTT-Epi Cycling TA Non-inflamed Epi N7 Epi 1422 6884 N7.EpiA.GCGAGAGATCGTTT 0.107641 6884.0 1422 N7 8 proliferating transit amplifying cell epithelial cell 8: epithelial cell Epithelial
29 N7.EpiA.GGAACTTGTGGCAT-Epi Enterocytes Non-inflamed Epi N7 Epi 924 5051 N7.EpiA.GGAACTTGTGGCAT 0.072461 5051.0 924 N7 7 enterocyte enterocyte 7: enterocyte Epithelial
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
149702 N110.LPB.TTGAACGGTGCAACGA-Imm Plasma Inflamed LP N110 Imm 1246 8584 N110.LPB.TTGAACGGTGCAACGA 0.026445 8584.0 1246 N110 1 plasma cell plasma cell 1: plasma cell B_cells
149703 N110.LPB.TTGAACGTCACGCATA-Imm Plasma Inflamed LP N110 Imm 1198 7094 N110.LPB.TTGAACGTCACGCATA 0.020863 7094.0 1198 N110 2 plasma cell plasma cell 2: plasma cell B_cells
149704 N110.LPB.TTGAACGTCCACTGGG-Imm Plasma Inflamed LP N110 Imm 1179 7678 N110.LPB.TTGAACGTCCACTGGG 0.011071 7678.0 1179 N110 2 plasma cell plasma cell 2: plasma cell B_cells
149705 N110.LPB.TTGAACGTCGTACGGC-Imm CD8+ LP Inflamed LP N110 Imm 860 2072 N110.LPB.TTGAACGTCGTACGGC 0.057432 2072.0 860 N110 3 CD8-positive, alpha-beta T cell T cell or ILC 3: T cell or ILC T_cells
149706 N110.LPB.TTGACTTCATCCTAGA-Imm Plasma Inflamed LP N110 Imm 1420 9090 N110.LPB.TTGACTTCATCCTAGA 0.016832 9090.0 1420 N110 2 plasma cell plasma cell 2: plasma cell B_cells
149707 N110.LPB.TTGACTTTCGTACGGC-Imm Plasma Inflamed LP N110 Imm 1588 11496 N110.LPB.TTGACTTTCGTACGGC 0.012961 11496.0 1588 N110 2 plasma cell plasma cell 2: plasma cell B_cells
149708 N110.LPB.TTGCCGTAGAGCAATT-Imm CD4+ Activated Fos-lo Inflamed LP N110 Imm 814 2466 N110.LPB.TTGCCGTAGAGCAATT 0.027981 2466.0 814 N110 3 activated CD4-positive, alpha-beta T cell T cell or ILC 3: T cell or ILC T_cells
149709 N110.LPB.TTGCCGTAGTCAAGCG-Imm Plasma Inflamed LP N110 Imm 1223 6920 N110.LPB.TTGCCGTAGTCAAGCG 0.016763 6920.0 1223 N110 2 plasma cell plasma cell 2: plasma cell B_cells
149710 N110.LPB.TTGCCGTGTCAGATAA-Imm Plasma Inflamed LP N110 Imm 1672 13511 N110.LPB.TTGCCGTGTCAGATAA 0.014063 13511.0 1672 N110 2 plasma cell plasma cell 2: plasma cell B_cells
149711 N110.LPB.TTGCCGTGTGTGTGCC-Imm Plasma Inflamed LP N110 Imm 1499 11399 N110.LPB.TTGCCGTGTGTGTGCC 0.011405 11399.0 1499 N110 2 plasma cell plasma cell 2: plasma cell B_cells
149712 N110.LPB.TTGCCGTTCAAAGACA-Imm Plasma Inflamed LP N110 Imm 1036 5960 N110.LPB.TTGCCGTTCAAAGACA 0.021980 5960.0 1036 N110 2 plasma cell plasma cell 2: plasma cell B_cells
149713 N110.LPB.TTGCGTCAGCTCCTTC-Imm Follicular Inflamed LP N110 Imm 853 2033 N110.LPB.TTGCGTCAGCTCCTTC 0.052632 2033.0 853 N110 10 follicular B cell B cell 10: B cell B_cells
149714 N110.LPB.TTGGAACCATGCCTTC-Imm Plasma Inflamed LP N110 Imm 895 5828 N110.LPB.TTGGAACCATGCCTTC 0.012011 5828.0 895 N110 2 plasma cell plasma cell 2: plasma cell B_cells
149715 N110.LPB.TTGGAACTCTCTGTCG-Imm Plasma Inflamed LP N110 Imm 1313 8122 N110.LPB.TTGGAACTCTCTGTCG 0.019576 8122.0 1313 N110 2 plasma cell plasma cell 2: plasma cell B_cells
149716 N110.LPB.TTGTAGGTCCTTGACC-Imm Plasma Inflamed LP N110 Imm 837 4026 N110.LPB.TTGTAGGTCCTTGACC 0.034526 4026.0 837 N110 2 plasma cell plasma cell 2: plasma cell B_cells
149717 N110.LPB.TTTACTGAGAACAACT-Imm Plasma Inflamed LP N110 Imm 1102 7834 N110.LPB.TTTACTGAGAACAACT 0.013786 7834.0 1102 N110 1 plasma cell plasma cell 1: plasma cell B_cells
149718 N110.LPB.TTTACTGTCTACGAGT-Imm Plasma Inflamed LP N110 Imm 1432 9233 N110.LPB.TTTACTGTCTACGAGT 0.014946 9233.0 1432 N110 2 plasma cell plasma cell 2: plasma cell B_cells
149719 N110.LPB.TTTATGCAGACGCACA-Imm Plasma Inflamed LP N110 Imm 1343 9698 N110.LPB.TTTATGCAGACGCACA 0.017014 9698.0 1343 N110 2 plasma cell plasma cell 2: plasma cell B_cells
149720 N110.LPB.TTTATGCAGTACTTGC-Imm Cycling Monocytes Inflamed LP N110 Imm 2101 6771 N110.LPB.TTTATGCAGTACTTGC 0.058189 6771.0 2101 N110 12 proliferating monocyte macrophage 12: macrophage Myeloid
149721 N110.LPB.TTTATGCGTTTACTCT-Imm Plasma Inflamed LP N110 Imm 1166 7139 N110.LPB.TTTATGCGTTTACTCT 0.021151 7139.0 1166 N110 2 plasma cell plasma cell 2: plasma cell B_cells
149722 N110.LPB.TTTATGCTCCGCGTTT-Imm Macrophages Inflamed LP N110 Imm 1545 5224 N110.LPB.TTTATGCTCCGCGTTT 0.043453 5224.0 1545 N110 12 macrophage macrophage 12: macrophage Myeloid
149723 N110.LPB.TTTATGCTCTTGGGTA-Imm Plasma Inflamed LP N110 Imm 959 5389 N110.LPB.TTTATGCTCTTGGGTA 0.017257 5389.0 959 N110 4 plasma cell plasma cell 4: plasma cell B_cells
149724 N110.LPB.TTTCCTCAGCGCTCCA-Imm Plasma Inflamed LP N110 Imm 947 5470 N110.LPB.TTTCCTCAGCGCTCCA 0.024314 5470.0 947 N110 2 plasma cell plasma cell 2: plasma cell B_cells
149725 N110.LPB.TTTCCTCAGTACGACG-Imm Plasma Inflamed LP N110 Imm 1164 6099 N110.LPB.TTTCCTCAGTACGACG 0.020659 6099.0 1164 N110 4 plasma cell plasma cell 4: plasma cell B_cells
149726 N110.LPB.TTTCCTCTCAAAGACA-Imm Plasma Inflamed LP N110 Imm 911 4672 N110.LPB.TTTCCTCTCAAAGACA 0.034461 4672.0 911 N110 2 plasma cell plasma cell 2: plasma cell B_cells
149727 N110.LPB.TTTGCGCAGGGTTCCC-Imm Macrophages Inflamed LP N110 Imm 1172 3549 N110.LPB.TTTGCGCAGGGTTCCC 0.063398 3549.0 1172 N110 12 macrophage macrophage 12: macrophage Myeloid
149728 N110.LPB.TTTGCGCCATGTCGAT-Imm Plasma Inflamed LP N110 Imm 1356 9534 N110.LPB.TTTGCGCCATGTCGAT 0.019194 9534.0 1356 N110 2 plasma cell plasma cell 2: plasma cell B_cells
149729 N110.LPB.TTTGCGCTCAACGAAA-Imm CD4+ Activated Fos-hi Inflamed LP N110 Imm 858 2084 N110.LPB.TTTGCGCTCAACGAAA 0.051344 2084.0 858 N110 3 activated CD4-positive, alpha-beta T cell T cell or ILC 3: T cell or ILC T_cells
149730 N110.LPB.TTTGCGCTCAACGGCC-Imm Plasma Inflamed LP N110 Imm 1753 12962 N110.LPB.TTTGCGCTCAACGGCC 0.019981 12962.0 1753 N110 2 plasma cell plasma cell 2: plasma cell B_cells
149731 N110.LPB.TTTGTCAGTTGACGTT-Imm Macrophages Inflamed LP N110 Imm 965 2696 N110.LPB.TTTGTCAGTTGACGTT 0.051187 2696.0 965 N110 12 macrophage macrophage 12: macrophage Myeloid

149732 rows × 18 columns

In [12]:
adata_pred.obs
Out[12]:
CELL CONDITION Sample_geo_accession Sample_title Subject tissue status 10x chemistry Sample_relation Sample_relation_2 ... Lane Subtype percent_mito n_counts n_genes batch leiden dblabel celltype cluster_celltype
index
GSM3972009_69.AAACATACACACCA-1 GSM3972009_69.AAACATACACACCA-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 Central Memory T cells 0.012165 1233.0 500 pat. 5 0 CD4-positive, alpha-beta memory T cell T cell 0: T cell
GSM3972009_69.AAACATTGGTGTCA-1 GSM3972009_69.AAACATTGGTGTCA-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... unknown unknown 0.012548 4142.0 1277 pat. 5 12 fibroblast fibroblast 12: fibroblast
GSM3972009_69.AAACGCACTTAGGC-1 GSM3972009_69.AAACGCACTTAGGC-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 Activated fibroblasts 0.006716 5806.0 1727 pat. 5 12 fibroblast fibroblast 12: fibroblast
GSM3972009_69.AAACGCTGCTACCC-1 GSM3972009_69.AAACGCTGCTACCC-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 Tregs 0.010526 1327.0 627 pat. 5 5 regulatory T cell T cell 5: T cell
GSM3972009_69.AAACTTGAGTCACA-1 GSM3972009_69.AAACTTGAGTCACA-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 Pericytes 0.013407 3803.0 1327 pat. 5 21 pericyte cell pericyte cell 21: pericyte cell
GSM3972009_69.AAACTTGATCACCC-1 GSM3972009_69.AAACTTGATCACCC-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 IgA plasma cells 0.006319 6330.0 864 pat. 5 11 IgG plasma cell plasma cell 11: plasma cell
GSM3972009_69.AAAGACGAATCACG-1 GSM3972009_69.AAAGACGAATCACG-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 Plasmablasts 0.015349 10294.0 2204 pat. 5 19 proliferating T cell T cell 19: T cell
GSM3972009_69.AAAGACGAATGCTG-1 GSM3972009_69.AAAGACGAATGCTG-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 Resident macrophages 0.027449 1858.0 644 pat. 5 6 myeloid leukocyte myeloid leukocyte 6: myeloid leukocyte
GSM3972009_69.AAAGATCTGTATCG-1 GSM3972009_69.AAAGATCTGTATCG-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 DC2 0.017936 2732.0 870 pat. 5 6 myeloid leukocyte myeloid leukocyte 6: myeloid leukocyte
GSM3972009_69.AAAGATCTTATCGG-1 GSM3972009_69.AAAGATCTTATCGG-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 IgG plasma cells 0.004392 15480.0 920 pat. 5 11 IgG plasma cell plasma cell 11: plasma cell
GSM3972009_69.AAAGCAGAGGTTCA-1 GSM3972009_69.AAAGCAGAGGTTCA-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 DC1 0.016954 3657.0 875 pat. 5 6 myeloid leukocyte myeloid leukocyte 6: myeloid leukocyte
GSM3972009_69.AAAGCAGATTGGCA-1 GSM3972009_69.AAAGCAGATTGGCA-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 Plasmablasts 0.019023 5467.0 1233 pat. 5 11 IgG plasma cell plasma cell 11: plasma cell
GSM3972009_69.AAAGCAGATTTCGT-1 GSM3972009_69.AAAGCAGATTTCGT-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 ACKR1+ endothelial cells 0.015983 1438.0 692 pat. 5 14 blood vessel endothelial cell endothelial cell 14: endothelial cell
GSM3972009_69.AAAGCCTGACTGTG-1 GSM3972009_69.AAAGCCTGACTGTG-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 Activated fibroblasts 0.087591 1643.0 816 pat. 5 12 fibroblast fibroblast 12: fibroblast
GSM3972009_69.AAAGCCTGAGCCTA-1 GSM3972009_69.AAAGCCTGAGCCTA-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 Central Memory T cells 0.017105 1520.0 595 pat. 5 3 naive T cell T cell 3: T cell
GSM3972009_69.AAAGTTTGTCTAGG-1 GSM3972009_69.AAAGTTTGTCTAGG-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 Activated fibroblasts 0.013503 7848.0 1974 pat. 5 12 fibroblast fibroblast 12: fibroblast
GSM3972009_69.AAATCAACTTCTTG-1 GSM3972009_69.AAATCAACTTCTTG-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 IgG plasma cells 0.004730 6342.0 847 pat. 5 11 IgG plasma cell plasma cell 11: plasma cell
GSM3972009_69.AAATCATGAATGCC-1 GSM3972009_69.AAATCATGAATGCC-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 IgG plasma cells 0.002807 16389.0 1288 pat. 5 11 IgG plasma cell plasma cell 11: plasma cell
GSM3972009_69.AAATCCCTGTCGTA-1 GSM3972009_69.AAATCCCTGTCGTA-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 IgG plasma cells 0.006611 8923.0 930 pat. 5 11 IgG plasma cell plasma cell 11: plasma cell
GSM3972009_69.AAATCTGAGCTAAC-1 GSM3972009_69.AAATCTGAGCTAAC-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 IgG plasma cells 0.015385 12282.0 1639 pat. 5 6 myeloid leukocyte myeloid leukocyte 6: myeloid leukocyte
GSM3972009_69.AAATGGGAGGACAG-1 GSM3972009_69.AAATGGGAGGACAG-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 IgA plasma cells 0.007100 7746.0 971 pat. 5 10 IgM or IgA plasma cell plasma cell 10: plasma cell
GSM3972009_69.AAATGTTGGTGCTA-1 GSM3972009_69.AAATGTTGGTGCTA-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 Activated fibroblasts 0.027858 4519.0 1331 pat. 5 12 fibroblast fibroblast 12: fibroblast
GSM3972009_69.AAATTCGACAACCA-1 GSM3972009_69.AAATTCGACAACCA-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 IgG plasma cells 0.015620 3201.0 745 pat. 5 11 IgG plasma cell plasma cell 11: plasma cell
GSM3972009_69.AACAAACTGGTCAT-1 GSM3972009_69.AACAAACTGGTCAT-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 DC1 0.033011 1757.0 617 pat. 5 6 myeloid leukocyte myeloid leukocyte 6: myeloid leukocyte
GSM3972009_69.AACACGTGAAGATG-1 GSM3972009_69.AACACGTGAAGATG-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 IgG plasma cells 0.002581 13167.0 880 pat. 5 11 IgG plasma cell plasma cell 11: plasma cell
GSM3972009_69.AACACGTGTCGCTC-1 GSM3972009_69.AACACGTGTCGCTC-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 IgG plasma cells 0.005225 8230.0 710 pat. 5 11 IgG plasma cell plasma cell 11: plasma cell
GSM3972009_69.AACACTCTAGCAAA-1 GSM3972009_69.AACACTCTAGCAAA-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 Activated fibroblasts 0.013588 4340.0 1368 pat. 5 12 fibroblast fibroblast 12: fibroblast
GSM3972009_69.AACAGAGAATTTCC-1 GSM3972009_69.AACAGAGAATTTCC-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 IgG plasma cells 0.006489 3081.0 525 pat. 5 11 IgG plasma cell plasma cell 11: plasma cell
GSM3972009_69.AACAGCACTCAGGT-1 GSM3972009_69.AACAGCACTCAGGT-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 IgG plasma cells 0.004187 10508.0 887 pat. 5 11 IgG plasma cell plasma cell 11: plasma cell
GSM3972009_69.AACAGCACTGCACA-1 GSM3972009_69.AACAGCACTGCACA-1 Involved GSM3972009 Ileal Involved 69 pat. 5 ileal Involved V1 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 69.0 Central Memory T cells 0.015778 1331.0 533 pat. 5 5 regulatory T cell T cell 5: T cell
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
GSM3972030_209.TTTATGCCATTTGCCC-1 GSM3972030_209.TTTATGCCATTTGCCC-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 Th17 Trm 0.025601 3164.0 946 pat. 16 7 CD8-positive, alpha-beta memory T cell T cell 7: T cell
GSM3972030_209.TTTATGCGTGCATCTA-1 GSM3972030_209.TTTATGCGTGCATCTA-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 Tregs 0.020492 2928.0 901 pat. 16 5 regulatory T cell T cell 5: T cell
GSM3972030_209.TTTCCTCAGGGCACTA-1 GSM3972030_209.TTTCCTCAGGGCACTA-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 CD8 Trm 0.067949 1663.0 522 pat. 16 18 memory T cell T cell 18: T cell
GSM3972030_209.TTTCCTCAGTGGCACA-1 GSM3972030_209.TTTCCTCAGTGGCACA-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 Tregs 0.074179 1766.0 625 pat. 16 5 regulatory T cell T cell 5: T cell
GSM3972030_209.TTTCCTCCAGCTCGCA-1 GSM3972030_209.TTTCCTCCAGCTCGCA-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 Tregs 0.050861 2556.0 884 pat. 16 5 regulatory T cell T cell 5: T cell
GSM3972030_209.TTTCCTCCATTCACTT-1 GSM3972030_209.TTTCCTCCATTCACTT-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 CD8 Trm 0.075423 2307.0 813 pat. 16 1 CD8-positive, alpha-beta cytotoxic T cell T cell 1: T cell
GSM3972030_209.TTTCCTCGTAGATTAG-1 GSM3972030_209.TTTCCTCGTAGATTAG-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 Resident macrophages 0.048736 3837.0 1408 pat. 16 6 myeloid leukocyte myeloid leukocyte 6: myeloid leukocyte
GSM3972030_209.TTTCCTCGTCGCGGTT-1 GSM3972030_209.TTTCCTCGTCGCGGTT-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 CD8 Trm 0.026460 3477.0 1004 pat. 16 1 CD8-positive, alpha-beta cytotoxic T cell T cell 1: T cell
GSM3972030_209.TTTCCTCTCCTTCAAT-1 GSM3972030_209.TTTCCTCTCCTTCAAT-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 IgA plasma cells 0.013345 10116.0 1344 pat. 16 4 IgM or IgA plasma cell plasma cell 4: plasma cell
GSM3972030_209.TTTCCTCTCGAACTGT-1 GSM3972030_209.TTTCCTCTCGAACTGT-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 CD8 Trm 0.077309 1397.0 545 pat. 16 1 CD8-positive, alpha-beta cytotoxic T cell T cell 1: T cell
GSM3972030_209.TTTGCGCAGACGCACA-1 GSM3972030_209.TTTGCGCAGACGCACA-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 Fibroblasts 0.025401 3301.0 1504 pat. 16 12 fibroblast fibroblast 12: fibroblast
GSM3972030_209.TTTGCGCAGGTAGCCA-1 GSM3972030_209.TTTGCGCAGGTAGCCA-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 Memory B cells 0.052716 8744.0 2026 pat. 16 2 memory B cell B cell 2: B cell
GSM3972030_209.TTTGCGCCAAGTAATG-1 GSM3972030_209.TTTGCGCCAAGTAATG-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 Memory B cells 0.052926 3760.0 920 pat. 16 2 memory B cell B cell 2: B cell
GSM3972030_209.TTTGCGCCACGGACAA-1 GSM3972030_209.TTTGCGCCACGGACAA-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 CD8 Trm 0.034401 1686.0 605 pat. 16 1 CD8-positive, alpha-beta cytotoxic T cell T cell 1: T cell
GSM3972030_209.TTTGCGCGTCAGAATA-1 GSM3972030_209.TTTGCGCGTCAGAATA-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 Lymphatics 0.126883 2185.0 1064 pat. 16 23 HEV endothelial cell endothelial cell 23: endothelial cell
GSM3972030_209.TTTGCGCTCAGTCCCT-1 GSM3972030_209.TTTGCGCTCAGTCCCT-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 IgA plasma cells 0.020774 17618.0 1489 pat. 16 13 IgM or IgA plasma cell plasma cell 13: plasma cell
GSM3972030_209.TTTGCGCTCCAGTAGT-1 GSM3972030_209.TTTGCGCTCCAGTAGT-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 Tregs 0.043265 2034.0 708 pat. 16 5 regulatory T cell T cell 5: T cell
GSM3972030_209.TTTGGTTCAAAGCGGT-1 GSM3972030_209.TTTGGTTCAAAGCGGT-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 CD8 Trm 0.067089 2370.0 878 pat. 16 1 CD8-positive, alpha-beta cytotoxic T cell T cell 1: T cell
GSM3972030_209.TTTGGTTCAATGTTGC-1 GSM3972030_209.TTTGGTTCAATGTTGC-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 DC1 0.079333 8395.0 1970 pat. 16 6 myeloid leukocyte myeloid leukocyte 6: myeloid leukocyte
GSM3972030_209.TTTGGTTCATTCCTGC-1 GSM3972030_209.TTTGGTTCATTCCTGC-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 Memory B cells 0.056118 4150.0 1165 pat. 16 2 memory B cell B cell 2: B cell
GSM3972030_209.TTTGGTTGTGTAATGA-1 GSM3972030_209.TTTGGTTGTGTAATGA-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 Th17 Trm 0.031838 5370.0 1679 pat. 16 0 CD4-positive, alpha-beta memory T cell T cell 0: T cell
GSM3972030_209.TTTGGTTTCAAACGGG-1 GSM3972030_209.TTTGGTTTCAAACGGG-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 IgA plasma cells 0.060678 7136.0 1289 pat. 16 13 IgM or IgA plasma cell plasma cell 13: plasma cell
GSM3972030_209.TTTGGTTTCCTGCAGG-1 GSM3972030_209.TTTGGTTTCCTGCAGG-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 Th17 Trm 0.000573 3493.0 1213 pat. 16 0 CD4-positive, alpha-beta memory T cell T cell 0: T cell
GSM3972030_209.TTTGTCAAGCATCATC-1 GSM3972030_209.TTTGTCAAGCATCATC-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 CD8 Trm 0.121032 1512.0 533 pat. 16 18 memory T cell T cell 18: T cell
GSM3972030_209.TTTGTCAAGGTGATTA-1 GSM3972030_209.TTTGTCAAGGTGATTA-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 IgA plasma cells 0.024231 11802.0 1626 pat. 16 13 IgM or IgA plasma cell plasma cell 13: plasma cell
GSM3972030_209.TTTGTCAGTCTCCCTA-1 GSM3972030_209.TTTGTCAGTCTCCCTA-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 IgA plasma cells 0.048219 4998.0 795 pat. 16 10 IgM or IgA plasma cell plasma cell 10: plasma cell
GSM3972030_209.TTTGTCAGTCTCTTAT-1 GSM3972030_209.TTTGTCAGTCTCTTAT-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 CD8 Trm 0.031284 1822.0 749 pat. 16 1 CD8-positive, alpha-beta cytotoxic T cell T cell 1: T cell
GSM3972030_209.TTTGTCAGTGTGGTTT-1 GSM3972030_209.TTTGTCAGTGTGGTTT-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 ILC3 0.100821 2190.0 740 pat. 16 16 group 3 innate lymphoid cell ILC3 16: ILC3
GSM3972030_209.TTTGTCATCAGTTAGC-1 GSM3972030_209.TTTGTCATCAGTTAGC-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 Trm 0.040230 1740.0 611 pat. 16 0 CD4-positive, alpha-beta memory T cell T cell 0: T cell
GSM3972030_209.TTTGTCATCGTCCAGG-1 GSM3972030_209.TTTGTCATCGTCCAGG-1 Involved GSM3972030 Ileal Involved 209 pat. 16 ileal Involved V2 BioSample: https://www.ncbi.nlm.nih.gov/biosam... SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... ... 209.0 CD8 Trm 0.030513 2884.0 976 pat. 16 1 CD8-positive, alpha-beta cytotoxic T cell T cell 1: T cell

62202 rows × 27 columns

In [ ]:
 

This function merges training datasets, removes unwanted genes, and if scanorama is used corrects for datasets.

In [13]:
adata_train, adata_pred = bc.tl.auto_annot.merge_data(adata_trains, adata_pred, genes_to_use = genes_to_use, merge = merge)
merging with scanorama
using scanorama rn
Found 1054 genes among all datasets
[[0.         0.55768303]
 [0.         0.        ]]
Processing datasets (0, 1)
integrating training set
calculating intersection

Train the classifier.

The returned scaler is fitted on the training dataset (to zero mean and scaled to unit variance).

In [14]:
classifier, scaler = bc.tl.auto_annot.fit(adata_train, method, celltype)
[Parallel(n_jobs=10)]: Using backend LokyBackend with 10 concurrent workers.
[Parallel(n_jobs=10)]: Done   5 out of   5 | elapsed: 11.9min finished
./conda/envs/besca_test/lib/python3.6/site-packages/sklearn/linear_model/_logistic.py:940: ConvergenceWarning:

lbfgs failed to converge (status=1):
STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.

Increase the number of iterations (max_iter) or scale the data as shown in:
    https://scikit-learn.org/stable/modules/preprocessing.html
Please also refer to the documentation for alternative solver options:
    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression

Prediction

Use fitted model to predict celltypes in adata_pred. Prediction will be added in a new column called 'auto_annot'. Paths are needed as adata_pred will revert to its original state (all genes, no additional corrections). The threshold should be set to 0 or left out for SVM. For logisitic regression the threshold can be set.

In [15]:
adata_predicted = bc.tl.auto_annot.adata_predict(classifier = classifier, scaler = scaler, adata_pred = adata_pred, adata_orig = adata_orig, threshold = 0.1)

Write out metrics to a report file, create confusion matrices and comparative umap plots

In [16]:
%matplotlib inline


bc.tl.auto_annot.report(adata_predicted, celltype, method, analysis_name, train_datasets, test_dataset, False, merge, use_raw, genes_to_use, clustering = 'leiden')
./conda/envs/besca_test/lib/python3.6/site-packages/sklearn/metrics/_classification.py:1272: UndefinedMetricWarning:

Precision and F-score are ill-defined and being set to 0.0 in labels with no predicted samples. Use `zero_division` parameter to control this behavior.

./conda/envs/besca_test/lib/python3.6/site-packages/sklearn/metrics/_classification.py:1272: UndefinedMetricWarning:

Recall and F-score are ill-defined and being set to 0.0 in labels with no true samples. Use `zero_division` parameter to control this behavior.

... storing 'auto_annot' as categorical
WARNING: saving figure to file figures/umap.ondata_auto_annot_Martin2019_with_Smillie2019_Type.png
WARNING: saving figure to file figures/umap.auto_annot_Martin2019_with_Smillie2019_Type.png
Confusion matrix, without normalization
Normalized confusion matrix
In [17]:
import scanpy as sc
sc.pl.umap(adata_predicted, color=[celltype, 'auto_annot'])
sc.pl.umap(adata_predicted, color=[celltype, 'auto_annot'], legend_loc='on data', legend_fontsize=8)
In [18]:
adata_train
Out[18]:
View of AnnData object with n_obs × n_vars = 149732 × 1054 
    obs: 'CELL', 'Cluster', 'Health', 'Location', 'Subject', 'celltype_highlevel', 'nGene', 'nUMI', 'original_name', 'percent_mito', 'n_counts', 'n_genes', 'batch', 'leiden', 'dblabel', 'celltype', 'cluster_celltype', 'Type'
    var: 'ENSEMBL-0', 'SYMBOL', 'n_cells-0', 'total_counts-0', 'frac_reads-0', 'ENSEMBL-1', 'n_cells-1', 'total_counts-1', 'frac_reads-1'
In [ ]: